Multiple protein systems

Proteomics provides a unique insight on a global protein-system level into the basic molecular mechanisms that participate in the formation of a pituitary adenoma. Through our series of comparative proteomics, we have confirmed our initial hypothesis that the proteome differs between pituitary controls and adenomas— many DEPs were found that correlated to the comparative transcriptomics data and to the corresponding biological systems. Those protein systems summarized in Table 4 provide a hint of the multiple protein systems that are involved in the formation of a pituitary adenoma. Those DEPs provide a basis to determine the activities that are critical for the observed changes in expression—whether they occur either at the mRNA or protein level or by PTM, and whether they are involved in the formation of a human pituitary adenoma. 

Those data reveal an overview of multiple protein systems that could participate in human pituitary adenomas. 

Since many systems of interest in chemistry have intrinsic multiple time scales it is important to use integrators that deal efficiently with the multiple time scale problem. Since our multiple time step algorithm, the so-called reversible Reference System Propagator Algorithm (r-RESPA) [17, 24, 18, 26] is time reversible and symplectic, they are very useful in combination with HMC for constant temperature simulations of large protein systems. 

Frequency-selective REDOR (fsREDOR) is a very powerful technique developed for the study of 13C and 15N uniformly labeled peptides or proteins [92]. The basic idea of this technique is to combine REDOR and soft n pulses to recouple a selected 13C-15N dipole-dipole interaction in a multiple-spin system. Usually one could use Gaussian shaped pulses to achieve the required selective n inversions. Other band selective shaped pulses have been developed for a more uniform excitation profile [93]. In its original implementation, fsREDOR was used to extract the intemuclear distances of several model crystalline compounds [92], In the past few years, this technique has proven to be very useful for the study of amyloid fibrils as well. For the Ure2p10 39 fibril samples containing 13C and 15N uniformly... 

Huang, R.P, Detection of multiple proteins in an antibody-based protein microarray system, /. Immunol. Methods, 255, 1-13, 2001. 

It is often best to begin with purified proteins when studying the relationships between protein structure and function at the molecular level. The presence of multiple proteins often complicates data interpretation, as it is not clear if effects are due to protein interactions, variations in the ratio of proteins, or to other factors. In these studies it is advisable to select tests based on a fundamental physical or chemical property, since results are less likely to vary with the test conditions or instrumentation used. Unfortunately, it becomes less likely that the property under study will relate directly to function in a food system when such simplified (often dilute) systems are used. Something as seemingly insignificant as protein concentration in the model system can have a large influence on the results obtained. Also, the relative importance or contribution of a functional property to a complex food system can be misinterpreted in a purified model system. 

More recent trends aim in the direction of fabricating electrochemical protein array systems (for detecting multiple protein targets) and miniaturization of such immunoassays. These include an electrochemical protein chip with an array of 36 platinum electrodes on a glass substrate (64) and electrical immunoassays using microcavity formats down to the zmol antigen level (65). 

A key constraint in characterizing the products of these cDNAs is that often these sequences have no known function. Therefore, in expressing these cDNAs as recombinant proteins, one does not have an assay for activity to follow purification. Consequently, efforts to express these recombinant proteins rely on fusion constructs, multiple expression systems, and purification schemes that depend entirely on the presence of affinity tags. Expression and purification methods are designed to be independent of the characteristics of the protein of interest. 

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